Variant report

Variant	rs7977362
Chromosome Location	chr12:20672963-20672964
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11045273	1.00[CHB][hapmap]
rs11613220	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12832108	0.88[ASW][hapmap];1.00[CEU][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4762764	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4762968	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4762973	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6487099	0.90[CEU][hapmap];1.00[CHB][hapmap];0.86[GIH][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7134968	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7295612	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7303852	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7484304	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.82[TSI][hapmap];0.92[EUR][1000 genomes]
rs7487227	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7489188	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7953905	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1048067	chr12:20363755-20874845	Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv541408	chr12:20363755-20874845	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv1046870	chr12:20509914-20711535	Active TSS Genic enhancers Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases
4	nsv541409	chr12:20509914-20711535	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases
5	nsv1043890	chr12:20659151-21309993	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
6	nsv541410	chr12:20659151-21309993	Flanking Bivalent TSS/Enh Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7977362	DGCR5	trans	parietal	SCAN
rs7977362	ST8SIA1	cis	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:20661200-20673200	Weak transcription	NHDF-Ad	bronchial
2	chr12:20662400-20674600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr12:20667400-20673800	Weak transcription	A549	lung
4	chr12:20667600-20680200	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr12:20668200-20673600	Weak transcription	Aorta	Aorta
6	chr12:20670200-20673200	Weak transcription	Colon Smooth Muscle	Colon
7	chr12:20670600-20674600	Weak transcription	Fetal Intestine Small	intestine
8	chr12:20670800-20679400	Weak transcription	Rectal Smooth Muscle	rectum
9	chr12:20671000-20675600	Weak transcription	Osteobl	bone
10	chr12:20671000-20679800	Weak transcription	Stomach Smooth Muscle	stomach
11	chr12:20671400-20673000	Weak transcription	Ovary	ovary
12	chr12:20671800-20674800	Strong transcription	Hela-S3	cervix
13	chr12:20672200-20675000	Enhancers	Left Ventricle	heart
14	chr12:20672600-20673800	Enhancers	iPS-15b Cell Line	embryonic stem cell
15	chr12:20672600-20674000	Enhancers	Fetal Muscle Leg	muscle
16	chr12:20672600-20674000	Enhancers	Right Ventricle	heart
17	chr12:20672800-20673000	Enhancers	HUES48 Cell Line	embryonic stem cell
18	chr12:20672800-20673000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr12:20672800-20673000	Enhancers	Right Atrium	heart
20	chr12:20672800-20673800	Strong transcription	Fetal Intestine Large	intestine

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